High-density single nucleotide polymorphism markers reveal the population structure of 2 local chicken genetic resources
ABSTRACT: Italy counts a large number of local chicken populations, some without a recognized genetic structure, such as Val Platani (VPL) and Cornuta (COS), which represent noteworthy local genetic resources. In this study, the genotype data of 34 COS and 42 VPL, obtained with the Affymetrix Axiom6...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-07-01
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| Series: | Poultry Science |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S0032579123002146 |
| _version_ | 1797802292049608704 |
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| author | Marco Tolone Maria Teresa Sardina Andrea Criscione Emiliano Lasagna Gabriele Senczuk Ilaria Rizzuto Silvia Riggio Angelo Moscarelli Vito Macaluso Rosalia Di Gerlando Martino Cassandro Baldassare Portolano Salvatore Mastrangelo |
| author_facet | Marco Tolone Maria Teresa Sardina Andrea Criscione Emiliano Lasagna Gabriele Senczuk Ilaria Rizzuto Silvia Riggio Angelo Moscarelli Vito Macaluso Rosalia Di Gerlando Martino Cassandro Baldassare Portolano Salvatore Mastrangelo |
| author_sort | Marco Tolone |
| collection | DOAJ |
| description | ABSTRACT: Italy counts a large number of local chicken populations, some without a recognized genetic structure, such as Val Platani (VPL) and Cornuta (COS), which represent noteworthy local genetic resources. In this study, the genotype data of 34 COS and 42 VPL, obtained with the Affymetrix Axiom600KChicken Genotyping Array, were used with the aim to investigate the genetic diversity, the runs of homozygosity (ROH) pattern, as well as the population structure and relationship within the framework of other local Italian and commercial chickens. The genetic diversity indices, estimated using different approaches, displayed moderate levels of genetic diversity in both populations. The identified ROH hotspots harbored genes related to immune response and adaptation to local hot temperatures. The results on genetic relationship and population structure reported a clear clustering of the populations according to their geographic origin. The COS formed a nonoverlapping genomic cluster and clearly separated from the other populations, but showed evident proximity to the Siciliana breed (SIC). The VPL highlighted intermediate relationships between the COS-SIC group and the rest of the sample, but closer to the other Italian local chickens. Moreover, VPL showed a complex genomic structure, highlighting the presence of 2 subpopulations that match with the different source of the samples. The results obtained from the survey on genetic differentiation underline the hypothesis that Cornuta is a population with a defined genetic structure. The substructure that characterizes the Val Platani chicken is probably the consequence of the combined effects of genetic drift, small population size, reproductive isolation, and inbreeding. These findings contribute to the understanding of genetic diversity and population structure, and represent a starting point for designing programs to monitor and safeguard these local genetic resources, in order to define a possible official recognition program as breeds. |
| first_indexed | 2024-03-13T05:03:30Z |
| format | Article |
| id | doaj.art-21cf9968892b45e1af4e31abe3c4b2c1 |
| institution | Directory Open Access Journal |
| issn | 0032-5791 |
| language | English |
| last_indexed | 2024-03-13T05:03:30Z |
| publishDate | 2023-07-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Poultry Science |
| spelling | doaj.art-21cf9968892b45e1af4e31abe3c4b2c12023-06-17T05:17:17ZengElsevierPoultry Science0032-57912023-07-011027102692High-density single nucleotide polymorphism markers reveal the population structure of 2 local chicken genetic resourcesMarco Tolone0Maria Teresa Sardina1Andrea Criscione2Emiliano Lasagna3Gabriele Senczuk4Ilaria Rizzuto5Silvia Riggio6Angelo Moscarelli7Vito Macaluso8Rosalia Di Gerlando9Martino Cassandro10Baldassare Portolano11Salvatore Mastrangelo12Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, ItalyDepartment of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, ItalyDepartment of Agriculture, Food and the Environment, University of Catania, 95131 Catania, ItalyDepartment of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, ItalyDepartment of Agricultural, Environmental and Food Sciences, University of Molise, 86100 Campobasso, ItalyDepartment of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, ItalyDepartment of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, ItalyDepartment of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, ItalyDepartment of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, ItalyDepartment of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, ItalyDepartment of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, ItalyDepartment of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, ItalyDepartment of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; Corresponding author:ABSTRACT: Italy counts a large number of local chicken populations, some without a recognized genetic structure, such as Val Platani (VPL) and Cornuta (COS), which represent noteworthy local genetic resources. In this study, the genotype data of 34 COS and 42 VPL, obtained with the Affymetrix Axiom600KChicken Genotyping Array, were used with the aim to investigate the genetic diversity, the runs of homozygosity (ROH) pattern, as well as the population structure and relationship within the framework of other local Italian and commercial chickens. The genetic diversity indices, estimated using different approaches, displayed moderate levels of genetic diversity in both populations. The identified ROH hotspots harbored genes related to immune response and adaptation to local hot temperatures. The results on genetic relationship and population structure reported a clear clustering of the populations according to their geographic origin. The COS formed a nonoverlapping genomic cluster and clearly separated from the other populations, but showed evident proximity to the Siciliana breed (SIC). The VPL highlighted intermediate relationships between the COS-SIC group and the rest of the sample, but closer to the other Italian local chickens. Moreover, VPL showed a complex genomic structure, highlighting the presence of 2 subpopulations that match with the different source of the samples. The results obtained from the survey on genetic differentiation underline the hypothesis that Cornuta is a population with a defined genetic structure. The substructure that characterizes the Val Platani chicken is probably the consequence of the combined effects of genetic drift, small population size, reproductive isolation, and inbreeding. These findings contribute to the understanding of genetic diversity and population structure, and represent a starting point for designing programs to monitor and safeguard these local genetic resources, in order to define a possible official recognition program as breeds.http://www.sciencedirect.com/science/article/pii/S0032579123002146SNPgenetic diversitylocal populationinbreedingconservation |
| spellingShingle | Marco Tolone Maria Teresa Sardina Andrea Criscione Emiliano Lasagna Gabriele Senczuk Ilaria Rizzuto Silvia Riggio Angelo Moscarelli Vito Macaluso Rosalia Di Gerlando Martino Cassandro Baldassare Portolano Salvatore Mastrangelo High-density single nucleotide polymorphism markers reveal the population structure of 2 local chicken genetic resources Poultry Science SNP genetic diversity local population inbreeding conservation |
| title | High-density single nucleotide polymorphism markers reveal the population structure of 2 local chicken genetic resources |
| title_full | High-density single nucleotide polymorphism markers reveal the population structure of 2 local chicken genetic resources |
| title_fullStr | High-density single nucleotide polymorphism markers reveal the population structure of 2 local chicken genetic resources |
| title_full_unstemmed | High-density single nucleotide polymorphism markers reveal the population structure of 2 local chicken genetic resources |
| title_short | High-density single nucleotide polymorphism markers reveal the population structure of 2 local chicken genetic resources |
| title_sort | high density single nucleotide polymorphism markers reveal the population structure of 2 local chicken genetic resources |
| topic | SNP genetic diversity local population inbreeding conservation |
| url | http://www.sciencedirect.com/science/article/pii/S0032579123002146 |
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